Sample summary

Barcode Alias Read count Median read length Contig count MLST Species call (ANI | Fraction query)
barcode01 test1 22031 5908.0 2 mycobacteria_2 Mycobacterium tuberculosis ( 0.999 | 0.970)
barcode02 test2 7076 3328.0 331 senterica_achtman_2 Salmonella enterica ( 0.987 | 0.523)
MLST: Multi-locus sequence typing
ANI: Average Nucleotide Identity
Fraction query: Fraction of query genome matched to reference

Read summary

Reads were filtered and summary statistics were generated using fastcat.
Use the dropdown menu to view different samples.

Assembly summary statistics

Assembly QC statistics reported by Flye following de novo assembly.
You can use the dropdown menu to view different samples.

Contig Length (bp) Coverage Circular Repeat Multiplicity
contig_1 4415551 34.0 N N 1
contig_2 113211 205.0 N Y 5
Contig Length (bp) Coverage Circular Repeat Multiplicity
contig_323 59596 6.0 N N 1
contig_277 42175 5.0 N N 1
contig_300 38841 4.0 N N 1
contig_316 35380 5.0 N N 1
contig_287 34854 5.0 N N 1
contig_315 34603 4.0 N N 1
contig_269 34317 5.0 N N 1
contig_297 33882 5.0 N N 1
contig_275 32126 4.0 N N 1
contig_285 31539 4.0 N N 1
contig_296 31004 5.0 N N 1
contig_1 29762 5.0 N N 1
contig_113 29247 7.0 N N 2
contig_319 28236 7.0 N N 2
contig_281 27573 6.0 N N 1
contig_25 26878 4.0 N N 1
contig_317 26274 6.0 N N 1
contig_302 25673 4.0 N N 1
contig_119 25580 6.0 N N 1
contig_331 25444 6.0 N N 1
contig_51 25439 7.0 N N 1
contig_311 25303 8.0 N N 2
contig_223 24704 5.0 N N 1
contig_318 24591 5.0 N N 1
contig_330 24534 5.0 N N 1
contig_262 23802 4.0 N N 1
contig_288 23637 6.0 N N 1
contig_270 23576 5.0 N N 1
contig_276 23568 6.0 N N 1
contig_75 23153 4.0 N N 1
contig_320 22817 5.0 N N 1
contig_21 22762 5.0 N N 1
contig_52 22592 5.0 N N 1
contig_193 22505 6.0 N N 1
contig_56 22289 4.0 N N 1
contig_263 22205 4.0 N N 1
contig_293 22192 6.0 N N 1
contig_133 22042 8.0 N N 2
contig_294 21953 3.0 N N 1
contig_132 21643 6.0 N N 1
contig_284 21360 4.0 N N 1
contig_271 21338 4.0 N N 1
contig_44 21017 4.0 N N 1
contig_295 20708 6.0 N N 1
contig_145 20451 3.0 N N 1
contig_91 20441 5.0 N N 1
contig_22 20381 3.0 N N 1
contig_153 20201 5.0 N N 1
contig_321 20123 6.0 N N 1
contig_282 19855 6.0 N N 1
contig_16 19789 9.0 N Y 2
contig_305 19577 5.0 N N 1
contig_15 19149 8.0 N N 2
contig_47 19125 5.0 N N 1
contig_134 18934 5.0 N N 1
contig_301 18578 3.0 N N 1
contig_197 18319 5.0 N N 1
contig_100 18287 4.0 N N 1
contig_252 18255 5.0 N N 1
contig_265 18224 5.0 N N 1
contig_298 18162 4.0 N N 1
contig_310 18154 6.0 N N 1
contig_226 18117 7.0 N N 2
contig_258 18029 5.0 N N 1
contig_77 17600 7.0 N N 2
contig_104 17430 7.0 N N 2
contig_309 17316 6.0 N N 1
contig_306 16929 5.0 N N 1
contig_57 16733 8.0 N N 2
contig_304 16709 5.0 N N 1
contig_278 16642 5.0 N N 1
contig_5 16549 4.0 N N 1
contig_103 16400 4.0 N N 1
contig_146 16321 4.0 N N 1
contig_244 16113 4.0 N N 1
contig_240 15921 5.0 N N 1
contig_128 15833 3.0 N N 1
contig_115 15785 4.0 N N 1
contig_70 15748 6.0 N N 1
contig_121 15504 3.0 N N 1
contig_261 15468 5.0 N N 1
contig_303 15315 5.0 N N 1
contig_208 15133 5.0 N N 1
contig_328 15014 4.0 N N 1
contig_246 14971 5.0 N N 1
contig_299 14936 6.0 N N 1
contig_255 14777 6.0 N N 1
contig_72 14707 5.0 N N 1
contig_247 14662 7.0 N N 2
contig_114 14635 6.0 N N 1
contig_283 14622 7.0 N N 1
contig_312 14290 5.0 N N 1
contig_13 14282 8.0 N N 2
contig_170 14191 3.0 N N 1
contig_118 13733 7.0 N N 1
contig_157 13727 6.0 N N 1
contig_34 13654 5.0 N N 1
contig_40 13617 5.0 N N 1
contig_207 13585 5.0 N N 1
contig_324 13357 5.0 N N 1
contig_313 13353 6.0 N N 1
contig_67 13204 5.0 N N 1
contig_46 13198 5.0 N N 1
contig_291 13059 5.0 N N 1
contig_192 13005 11.0 N Y 3
contig_166 12982 6.0 N N 1
contig_307 12974 10.0 N Y 2
contig_50 12740 5.0 N N 1
contig_36 12651 5.0 N N 1
contig_116 12613 6.0 N N 1
contig_14 12538 3.0 N N 1
contig_164 12358 4.0 N N 1
contig_280 12348 5.0 N N 1
contig_183 12345 7.0 N N 2
contig_88 12217 4.0 N N 1
contig_242 12195 5.0 N N 1
contig_8 12192 5.0 N N 1
contig_76 12161 5.0 N N 1
contig_259 12139 8.0 N N 2
contig_7 12138 4.0 N N 1
contig_272 12105 5.0 N N 1
contig_292 12031 4.0 N N 1
contig_102 12023 5.0 N N 1
contig_20 12014 6.0 N N 1
contig_181 11923 4.0 N N 1
contig_3 11818 3.0 N N 1
contig_159 11761 6.0 N N 1
contig_117 11742 6.0 N N 1
contig_122 11718 4.0 N N 1
contig_329 11503 4.0 N N 1
contig_160 11462 5.0 N N 1
contig_93 11459 5.0 N N 1
contig_9 11420 6.0 N N 1
contig_73 11412 5.0 N N 1
contig_154 11371 6.0 N N 1
contig_78 11326 7.0 N N 1
contig_82 11297 8.0 N N 2
contig_325 11131 5.0 N N 1
contig_314 11048 4.0 N N 1
contig_327 11015 5.0 N N 1
contig_221 10859 7.0 N N 2
contig_23 10656 5.0 N N 1
contig_2 10607 6.0 N N 1
contig_268 10533 5.0 N N 1
contig_289 10490 6.0 N N 1
contig_147 10480 4.0 N N 1
contig_161 10445 7.0 N N 2
contig_19 10294 4.0 N N 1
contig_182 10264 5.0 N N 1
contig_203 10240 5.0 N N 1
contig_31 10152 3.0 N N 1
contig_143 10088 3.0 N N 1
contig_127 10078 6.0 N N 1
contig_273 10062 6.0 N N 1
contig_41 9996 4.0 N N 1
contig_124 9984 5.0 N N 1
contig_308 9910 3.0 N N 1
contig_112 9862 7.0 N N 1
contig_326 9854 5.0 N N 1
contig_257 9839 6.0 N N 1
contig_266 9810 5.0 N N 1
contig_322 9773 7.0 N N 1
contig_49 9755 5.0 N N 1
contig_279 9611 4.0 N N 1
contig_81 9569 5.0 N N 1
contig_108 9459 4.0 N N 1
contig_169 9435 9.0 N Y 2
contig_138 9389 5.0 N N 1
contig_59 9351 4.0 N N 1
contig_267 9305 8.0 N N 2
contig_66 9234 5.0 N N 1
contig_250 9198 5.0 N N 1
contig_83 9189 6.0 N N 1
contig_253 9112 6.0 N N 1
contig_165 8880 3.0 N N 1
contig_97 8851 7.0 N N 2
contig_126 8793 6.0 N N 1
contig_71 8731 7.0 N N 2
contig_256 8703 5.0 N N 1
contig_26 8678 7.0 N N 1
contig_110 8633 3.0 N N 1
contig_142 8629 5.0 N N 1
contig_251 8466 4.0 N N 1
contig_64 8439 5.0 N N 1
contig_11 8361 4.0 N N 1
contig_176 8357 7.0 N N 2
contig_125 8281 6.0 N N 1
contig_129 8255 6.0 N N 1
contig_99 8244 4.0 N N 1
contig_173 8231 3.0 N N 1
contig_198 8204 4.0 N N 1
contig_39 8191 5.0 N N 1
contig_139 8145 5.0 N N 1
contig_196 8010 4.0 N N 1
contig_101 7993 7.0 N N 2
contig_152 7990 6.0 N N 1
contig_35 7958 4.0 N N 1
contig_227 7921 3.0 N N 1
contig_94 7884 4.0 N N 1
contig_4 7683 8.0 N N 2
contig_37 7665 4.0 N N 1
contig_74 7607 6.0 N N 1
contig_156 7588 7.0 N N 1
contig_195 7568 5.0 N N 1
contig_224 7563 4.0 N N 1
contig_155 7545 3.0 N N 1
contig_168 7535 4.0 N N 1
contig_10 7448 4.0 N N 1
contig_18 7356 8.0 N N 2
contig_130 7348 3.0 N N 1
contig_131 7297 4.0 N N 1
contig_43 7240 4.0 N N 1
contig_191 7229 4.0 N N 1
contig_6 7221 4.0 N N 1
contig_85 7207 4.0 N N 1
contig_123 7152 6.0 N N 1
contig_200 7076 6.0 N N 1
contig_243 7055 3.0 N N 1
contig_248 7055 9.0 N N 2
contig_120 7043 5.0 N N 1
contig_69 7034 8.0 N N 2
contig_201 6999 5.0 N N 1
contig_205 6972 5.0 N N 1
contig_254 6902 5.0 N N 1
contig_33 6835 6.0 N N 1
contig_92 6748 5.0 N N 1
contig_45 6737 5.0 N N 1
contig_55 6669 5.0 N N 1
contig_216 6646 3.0 N N 1
contig_239 6535 6.0 N N 1
contig_89 6509 7.0 N N 2
contig_109 6496 3.0 N N 1
contig_194 6469 5.0 N N 1
contig_105 6392 3.0 N N 1
contig_61 6370 6.0 N N 1
contig_228 6332 5.0 N N 1
contig_190 6315 6.0 N N 1
contig_187 6264 6.0 N N 1
contig_87 6264 6.0 N N 1
contig_137 6244 5.0 N N 1
contig_260 6237 5.0 N N 1
contig_38 6224 4.0 N N 1
contig_79 6214 6.0 N N 1
contig_213 6200 4.0 N N 1
contig_172 6196 3.0 N N 1
contig_211 6156 4.0 N N 1
contig_140 6046 4.0 N N 1
contig_175 6043 3.0 N N 1
contig_177 6002 6.0 N N 1
contig_144 6001 3.0 N N 1
contig_188 5971 4.0 N N 1
contig_98 5907 4.0 N N 1
contig_204 5861 4.0 N N 1
contig_90 5792 7.0 N N 2
contig_264 5790 5.0 N N 1
contig_32 5767 5.0 N N 1
contig_158 5759 4.0 N N 1
contig_17 5748 7.0 N N 1
contig_290 5715 4.0 N N 1
contig_62 5664 6.0 N N 1
contig_80 5647 7.0 N N 2
contig_219 5636 6.0 N N 1
contig_274 5597 39.0 N Y 10
contig_241 5461 8.0 N N 2
contig_231 5441 4.0 N N 1
contig_149 5429 4.0 N N 1
contig_286 5344 4.0 N N 1
contig_24 5245 5.0 N N 1
contig_58 5200 4.0 N N 1
contig_225 5142 5.0 N N 1
contig_234 5098 3.0 N N 1
contig_96 5057 5.0 N N 1
contig_202 5047 4.0 N N 1
contig_48 5038 5.0 N N 1
contig_30 5022 4.0 N N 1
contig_65 4996 3.0 N N 1
contig_60 4989 7.0 N N 1
contig_210 4984 3.0 N N 1
contig_54 4956 6.0 N N 1
contig_151 4893 5.0 N N 1
contig_29 4863 4.0 N N 1
contig_107 4824 3.0 N N 1
contig_162 4796 6.0 N N 1
contig_86 4700 4.0 N N 1
contig_232 4664 3.0 N N 1
contig_220 4629 5.0 N N 1
contig_141 4620 3.0 N N 1
contig_230 4597 3.0 N N 1
contig_12 4584 4.0 N N 1
contig_171 4584 5.0 N N 1
contig_84 4425 7.0 N N 1
contig_233 4420 3.0 N N 1
contig_42 4396 7.0 N N 1
contig_199 4382 6.0 N N 1
contig_249 4373 6.0 N N 1
contig_186 4114 3.0 N N 1
contig_167 4017 4.0 N N 1
contig_95 3998 4.0 N N 1
contig_215 3994 5.0 N N 1
contig_179 3973 3.0 N N 1
contig_180 3971 4.0 N N 1
contig_209 3958 3.0 N N 1
contig_174 3950 4.0 N N 1
contig_135 3935 5.0 N N 1
contig_235 3872 4.0 N N 1
contig_222 3828 5.0 N N 1
contig_245 3777 3.0 N N 1
contig_238 3709 3.0 N N 1
contig_185 3692 4.0 N N 1
contig_163 3670 6.0 N N 1
contig_218 3640 3.0 N N 1
contig_150 3484 7.0 N N 2
contig_136 3483 4.0 N N 1
contig_148 3442 4.0 N N 1
contig_63 3440 6.0 N N 1
contig_27 3422 4.0 N N 1
contig_189 3398 8.0 N N 1
contig_236 3319 3.0 N N 1
contig_214 3246 3.0 N N 1
contig_111 3223 9.0 N Y 2
contig_53 3178 4.0 N N 1
contig_206 2978 6.0 N N 1
contig_184 2976 5.0 N N 1
contig_229 2911 3.0 N N 1
contig_217 2904 3.0 N N 1
contig_237 2682 3.0 N N 1
contig_106 2617 7.0 N N 1
contig_212 2577 7.0 N N 1
contig_28 2455 4.0 N N 1
contig_178 2384 6.0 N N 1
contig_68 2250 3.0 N N 1

Plasmid identification

Plasmid identification was performed using MOB-suite
Use the dropdown menu to view different samples.
Click on each plasmid cluster to view detailed information about the contigs.

MOB-suite did not identify plasmid contigs in this assembly.

MOB-suite identified 3 plasmid contigs out of 331 total contigs in this assembly, representing 1 distinct plasmid.

Replicon type(s): -
Predicted mobility: non-mobilizable
Best database match (Mash distance): Salmonella enterica subsp. enterica ( 0.0377)
Predicted host range: genus Salmonella
Observed host range: genus Salmonella
Contig Length (bp) Replicon type Relaxase type MPF type oriT type
contig_44 20998 - - - -
contig_220 4627 - - - -
contig_42 4391 - - - -

Mash distance approaching 0 indicates close identity.

Antimicrobial resistance prediction

The assembly was analysed for presence of antimicrobial resistance genes and mutations using ResFinder.
You can use the dropdown menu to select different samples.

Resistance to the following antimicrobial and disinfectant classes was found:

Aldehyde Aminoglycoside Lincosamide Macrolide Quaternary Ammonium Compound Unspecified

Genes analysed for AMR point mutations:

ahpC-promoter alr drrA eis-promoter embA-promoter embB embC embR ethR fabG1-promoter folC gidB gyrA gyrB idsA2-promoter inhA iniA kasA katG-promoter nuoA-promoter panD pncA-promoter ribD rplC rpoB rpoC rpsA rpsL rrl rrs rv0678 thyA thyX-promoter tlyA ubiA
Known AMR mutations No known AMR mutations Region of interest not detected

Gene Drug(s) Contig Gene position Identity Coverage Accession PMID Database
formA Formaldehyde contig_1 498 - 1607 100.00% 100.00% X73835 8891129 DisinFinder

Gene Drug(s) Contig Gene position Identity Coverage Accession PMID Database
aac(2')-Ic Dibekacin, Gentamicin, Netilmicin, Tobramycin contig_1 314726 - 315271 100.00% 100.00% U72714 unpublished ResFinder

Gene Drug(s) Contig Gene position Identity Coverage Accession PMID Database
erm(37) Clindamycin, Lincomycin contig_1 2232096 - 2232635 100.00% 100.00% AL123456 9634230 ResFinder

Gene Drug(s) Contig Gene position Identity Coverage Accession PMID Database
erm(37) Erythromycin, Telithromycin contig_1 2232096 - 2232635 100.00% 100.00% AL123456 9634230 ResFinder

Gene Drug(s) Contig Gene position Identity Coverage Accession PMID Database
qacD Benzylkonium Chloride, Cetylpyridinium Chloride, Chlorhexidine, Ethidium Bromide contig_1 4411882 - 4413866 99.45% 98.80% M37888 1840534 DisinFinder

Gene Drug(s) Contig Gene position Identity Coverage Accession PMID Database
▸ embA-promoter (3) Ethambutol contig_1 4243534 - 4246933 99.88% 100.00% LR027516.1 - PointFinder
Mutation Drug(s) Position Nucleotide change Amino acid change PMID
n.-16C>T Ethambutol 4243518 C → T Promoter mutation 19209951
n.-12C>T Ethambutol 4243522 C → T Promoter mutation 19209951
n.-11C>A Ethambutol 4243523 C → A Promoter mutation 19209951

Resistance to the following antimicrobial and disinfectant classes was found:

Aminoglycoside Polymyxin

Genes analysed for AMR point mutations:

16S-rrsD acrB gyrA gyrB parC parE pmrA pmrB
Known AMR mutations No known AMR mutations Region of interest not detected

Gene Drug(s) Contig Gene position Identity Coverage Accession PMID Database
aac(6')-Iaa Amikacin, Tobramycin contig_312 4321 - 4758 98.63% 100.00% NC_003197 11677609 ResFinder

Gene Drug(s) Contig Gene position Identity Coverage Accession PMID Database
▸ pmrA (1) Colistin contig_302 14831 - 15499 99.10% 100.00% CP055130.1 - PointFinder
Mutation Drug(s) Position Nucleotide change Amino acid change PMID
p.G15R Colistin 14846 GGG → AGG G → R 19332669, 2550546

Multilocus sequence typing

Multilocus sequencing typing was performed using MLST. Typing scheme information is available at PubMLST.
You can use the dropdown menu to select different samples.

Scheme Sequence Type S8 S19 S12 L19 S7 S14Z L16 L35
mycobacteria_2 215 18 20 20 19 19 17 22 15
Scheme Sequence Type AroC SucA PurE DnaN HisD HemD ThrA
senterica_achtman_2 - 114 - ~1203 - 114 8 109

Salmonella serotyping

Serotyping was performed using SeqSero2.
You can use the dropdown menu to select different samples.

Serotyping is only available for isolates identified as Salmonella though MLST.
Predicted serotype Predicted antigenic profile O antigen prediction H1 antigen prediction(fliC) H2 antigen prediction(fljB) Note
Havana 13:f,g:- 13 f,g - nan

Genome coverage

The plot below illustrates depth of coverage. For adequate variant calling, depth should be at least 50X in any region.
Use the dropdown menu to select different samples.

Coverage for up to 20 longest contigs is displayed for each sample.

Software versions

Name Version
bakta 1.11.4
medaka 2.2.0
bcftools 1.21
mlst 2.23.0
sourmash 4.9.4
mob_recon 3.1.9
resfinder 4.7.2
SeqSero2 1.2.1
pysam 0.23.3
fastcat 0.22.1
bamstats 0.22.1
mosdepth 0.3.11
flye 2.9.5-b1801
dnaapler 1.2.0
pomoxis 0.3.16

Workflow parameters

Key Value
fastq wf-bacterial-genomes-demo/isolates_fastq
isolates True
sample_sheet wf-bacterial-genomes-demo/isolates_sample_sheet.csv
run_bakta False
bakta_db /data/wangdi/CGRProjects/ont/EBV/db
out_dir output
store_dir None
bam None
reference None
client_fields None
threads 3
chunk_size 1000000
bakta_opts None
bakta_db_type light
sample None
reference_based_assembly False
override_basecaller_cfg None
min_read_length 1000
max_coverage_plots 20
flye_opts None
flye_genome_size None
flye_asm_coverage None
run_plasmid_id True
plasmid_id_opts None
resfinder_threshold 0.8
resfinder_coverage 0.6
pointfinder_ignore_indels False
pointfinder_ignore_stop_codons False
resfinder_db None
pointfinder_db None
analyse_unclassified False
_sourmash_db_exclude_list /data/wangdi/.nextflow/25.10.0/assets/epi2me-labs/wf-bacterial-genomes/./data/sourmash_db_exclude_list.txt
_sourmash_pointfinder_mapping /data/wangdi/.nextflow/25.10.0/assets/epi2me-labs/wf-bacterial-genomes/./data/pointfinder_db_mapping.csv